X chromosome inactivation is a necessary process that occurs in XX individuals early in development. The X chromosome that will be inactivated expresses a long noncoding RNA molecule called Xist that recruits proteins to silence gene expression and to condense the chromosome. This process is described in more detail on the Scitable page about X-inactivation.

The specific X chromosome that is inactivated is somewhat random in each cell, but it can also be skewed towards the maternal or paternal chromosome. Inactivation skewing can be seen by studying human twins and by visualizing chromosome inactivation. X-inactivation has been visualized using genes for fluorescent proteins that were inserted into the two copies of the X chromosome in mice. This led to dramatic images that showed clusters of cells that all expressed one chromosome or a random distribution of cells, as explained in this blog. Random X-inactivation can also be seen in the pattern of fur coloration in calico cats.

X chromosome inactivation has important implications for the health of XX individuals, since the severity of an X-linked disease will depend on which X chromosome is expressed and where. For example, the gene for a necessary protein clotting factor is found on the X chromosome. A mutation in this gene that causes the protein to be nonfunctional will cause hemophilia (excessive bleeding) in XY individuals. However, in someone with two X chromosomes, who inherited one copy of the mutation, they may have hemophilia, or not, depending on which X chromosome is inactivated in the cells that produce this clotting factor. Just like with the colorblind twin, there is a case of identical twins, where one has hemophilia and other does not. The twin with hemophilia has skewed X-inactivation, so the good copy of the gene is on the inactivated chromosome, whereas the other twin has random X-inactivation and enough good copies of the gene are expressed to allow for normal blood clotting.

If you are interested in learning more about the details of X-inactivation and the implications for medicine, check out this comprehensive book called Females are Mosaics by Barbara R. Migeon.

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